So I’ve been working on the new Geoduck data analysis we have, and believe I’ve made progress!
Yesterday I started http://rpubs.com/seanb80/241330. The script should iterate through all of our samples, bringing them to the Methylation and SNP calling by Methyl Extract. I ran it over night and processed ~4.5 samples, so the 53 we have will take a while.
I spent the morning today working on the subsequent parts.
Relatedness from SNPs: http://rpubs.com/seanb80/241561
Merging multiple Methylation files: http://rpubs.com/seanb80/241581
Once this is done, we should have all of the parts to find differentially methylated regions!